SMED30027133

Overview
NameSMED30027133
Smed IDSMED30027133
Length (bp)1608
Neoblast Clusters

Zeng et. al., 2018




 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30027133

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30027133SMESG000018390.1 dd_Smed_v4_42506_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30027133 vs. Ensembl Zebrafish
Match: tg (thyroglobulin [Source:ZFIN;Acc:ZDB-GENE-030519-1])

HSP 1 Score: 52.7582 bits (125), Expect = 1.259e-6
Identity = 26/82 (31.71%), Postives = 42/82 (51.22%), Query Frame = 3
Query:  948 CIGTASLLDQENNQSCVLCGVGTFVAAFYAAVAMTYKKSGFCKLCPKNHYSDIEGNYECTPCPMGSSTKFEGSYNFSQCQSQ 1193
            C+   S L Q  +  CVLC  G+F +             G C  CP++ + + EG   C+PCP G+ST  +G+++ S C ++
Sbjct: 1414 CMTGYSQLPQ--STGCVLCPAGSFFSG------------GVCTPCPRDTFQEDEGQVFCSPCPAGTSTVAQGAFSASHCLTE 1481          
BLAST of SMED30027133 vs. Ensembl Zebrafish
Match: svep1 (sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 [Source:ZFIN;Acc:ZDB-GENE-110726-1])

HSP 1 Score: 50.8322 bits (120), Expect = 4.277e-6
Identity = 34/124 (27.42%), Postives = 61/124 (49.19%), Query Frame = 3
Query:  840 LKQTSNFIKDFFQRE-FQ--HFADRLVITNTTRFKSE---IFCIGTASLLDQENNQSCVLCGVGTFVAAFYAAVAMTYKKSGFCKLCPKNHYSDIEGNYECTPCPMGSSTKFEGSYNFSQCQSQ 1193
            L+Q +N +K    ++ F   H +  +++ +    +S+   ++C   + L      + CVLC VGT+ +  YA           C+ C +  Y + EG  EC  CP GSST +  S + ++C++Q
Sbjct:  948 LEQLTNRLKRTLAKQPFSTFHVSSEMIVADPKSLESKKATLYCRPGSVL----KGRVCVLCPVGTYFSLEYAE----------CESCWRGSYQNEEGQMECKSCPDGSSTPYLHSRSQAECKAQ 1057          
BLAST of SMED30027133 vs. TrEMBL
Match: A0A3B3T3R4 (Sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 OS=Paramormyrops kingsleyae OX=1676925 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 2.335e-6
Identity = 39/120 (32.50%), Postives = 56/120 (46.67%), Query Frame = 3
Query:  879 REFQHFADRLVIT------NTTRFKSEIFCIGTASLLDQENNQSC---------VLCGVGTFVAAFYAAVAMTYKKSGFCKLCPKNHYSDIEGNYECTPCPMGSSTKFEGSYNFSQCQSQ 1193
            R  +H  +RL  T      +T R  SE+      SL  Q+ +  C         +LC VGT+ +  +          G C+ C +  Y D+EG  ECTPCP GSST +  S + S+C+ Q
Sbjct:  887 RTLEHLTNRLKRTLSKQPLSTFRVDSEMIVADPKSLESQKASLFCRPGSVLKDRMLCPVGTYYSLEF----------GVCESCWRGSYQDLEGQTECTPCPDGSSTPYLHSRSLSECKEQ 996          
BLAST of SMED30027133 vs. Ensembl Cavefish
Match: svep1 (sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 [Source:NCBI gene;Acc:103042618])

HSP 1 Score: 57.3806 bits (137), Expect = 3.435e-8
Identity = 36/125 (28.80%), Postives = 59/125 (47.20%), Query Frame = 3
Query:  837 TLKQTSNFIKDFFQREFQ---HFADRLVITNTTRF---KSEIFCIGTASLLDQENNQSCVLCGVGTFVAAFYAAVAMTYKKSGFCKLCPKNHYSDIEGNYECTPCPMGSSTKFEGSYNFSQCQSQ 1193
            TL+Q +N +K    ++     H +  +++ +       K+ ++C   + L      + CV C VGTF +  YA           C+ C + +Y D EG  EC  CP G ST +  S N S+C++Q
Sbjct:  948 TLEQLTNRLKRTLSKQHINTFHVSSEMIVADPKSLESRKASLYCRPGSVL----KGRMCVQCPVGTFYSMEYAE----------CESCRRGYYQDEEGKTECKICPNGYSTPYLHSRNVSECKAQ 1058          
BLAST of SMED30027133 vs. Planmine SMEST
Match: SMESG000018390.1 (SMESG000018390.1)

HSP 1 Score: 387.882 bits (995), Expect = 4.511e-134
Identity = 189/195 (96.92%), Postives = 189/195 (96.92%), Query Frame = 3
Query:  165 MILIHSMVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRSYVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIHVNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQVRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLIVNISMDISY 749
            MILIHSMVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRSYVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIHVNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQVRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLI N     SY
Sbjct:    1 MILIHSMVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRSYVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIHVNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQVRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLIKNQYFGSSY 195          
BLAST of SMED30027133 vs. Planmine SMEST
Match: SMESG000018390.1 (SMESG000018390.1)

HSP 1 Score: 375.941 bits (964), Expect = 1.634e-129
Identity = 183/189 (96.83%), Postives = 183/189 (96.83%), Query Frame = 3
Query:  183 MVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRSYVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIHVNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQVRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLIVNISMDISY 749
            MVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRSYVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIHVNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQVRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLI N     SY
Sbjct:    1 MVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRSYVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIHVNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQVRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLIKNQYFGSSY 189          
BLAST of SMED30027133 vs. Planmine SMEST
Match: SMESG000018389.1 (SMESG000018389.1)

HSP 1 Score: 241.121 bits (614), Expect = 5.329e-78
Identity = 117/117 (100.00%), Postives = 117/117 (100.00%), Query Frame = 1
Query: 1117 MNVPHARWGRAQNLKDHTILANVKVKMKFTYKNYSQARKTMILGIMYFLPVLVIMVLWIVHNSFVTKNNLLNDIYDMQLELGKIVFMMKYKENQMKEMVNERRALSNEVYLTDSYEK 1467
            MNVPHARWGRAQNLKDHTILANVKVKMKFTYKNYSQARKTMILGIMYFLPVLVIMVLWIVHNSFVTKNNLLNDIYDMQLELGKIVFMMKYKENQMKEMVNERRALSNEVYLTDSYEK
Sbjct:    1 MNVPHARWGRAQNLKDHTILANVKVKMKFTYKNYSQARKTMILGIMYFLPVLVIMVLWIVHNSFVTKNNLLNDIYDMQLELGKIVFMMKYKENQMKEMVNERRALSNEVYLTDSYEK 117          
The following BLAST results are available for this feature:
BLAST of SMED30027133 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
tg1.259e-631.71thyroglobulin [Source:ZFIN;Acc:ZDB-GENE-030519-1][more]
svep14.277e-627.42sushi, von Willebrand factor type A, EGF and pentr... [more]
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BLAST of SMED30027133 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A3B3T3R42.335e-632.50Sushi, von Willebrand factor type A, EGF and pentr... [more]
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BLAST of SMED30027133 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
svep13.435e-828.80sushi, von Willebrand factor type A, EGF and pentr... [more]
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BLAST of SMED30027133 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30027133 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000018390.14.511e-13496.92SMESG000018390.1[more]
SMESG000018390.11.634e-12996.83SMESG000018390.1[more]
SMESG000018389.15.329e-78100.00SMESG000018389.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027133 ID=SMED30027133|Name=SMED30027133|organism=Schmidtea mediterranea sexual|type=transcript|length=1608bp
CTTCCGATCTCTTTATTCATCTGTTATTGACACAATTTTTTCATCTAAAT
GTGACCACCAGCCAGCGGTCCGTTATAAACCCTTCAATCAACGAGTATTA
CCAAACAAAAAATAGTAAACTTTATTATAAAAAAACCTTTACAACAATAT
TGGTCTATTATCATATGATTTTGATCCACTCAATGGTGACTTTATCTTGC
ATTGATCAACATGACAACCCATTTGGCAGTGATGTGTATTTGACAAATGT
CAGCTGGTTCAGTAAAGGTGAACCAATTTTCAAATCGGATTTTGTTCGCA
GTTACGTTGATCTTTTCGGATTTATTGCATTATTGCCTACCAAAAGTGGT
CAATTTCAAATTCTCTGTATTGGTAAATATAAGGACGTGAATGGAGCCAT
GAAAAACGCCAGCGTTGCACACATTTTCAATGTCAATGATTATTCAATTC
ATGTGAACTCTTTGAGTCTTGATCTTTCAGTAGCTTATTTTAAACAAAAT
AATGCTTCTATGACAAATGTCACTATTTCGGAGAGTGATCGTAGACTTCA
CTATAGAATATTTTTAGACAACAGAATTAAGCCGTGCTCTTTCTTGTTTC
AAGTTAGATTTAAAAAGAAAGTTGAATTATTTTACAGTCAAATATGCGTC
AGAAATCAACAGATTTGCGAGAGGGAATCCATTAATTTTTATGATTGCAC
TTATAATGAACTGGATTTAATTGTAAATATTTCTATGGATATTTCCTATT
ATTATGATTACAGAAAAATCAATATTTTGGCTCCAGTTATGGATTTCGAC
AACAAGAATGAAGGAGAAGCAAAGATACGAAATATGACTCTCAAACAAAC
GTCTAATTTTATTAAAGATTTCTTTCAAAGGGAATTTCAACATTTTGCAG
ATAGATTAGTTATTACAAATACAACTAGATTCAAATCTGAGATCTTCTGT
ATTGGAACCGCTTCTCTTTTGGATCAAGAAAATAATCAATCGTGTGTTCT
CTGTGGCGTTGGCACATTTGTTGCGGCTTTTTACGCTGCAGTGGCAATGA
CTTACAAAAAATCAGGATTCTGTAAGCTATGTCCAAAAAATCACTACTCT
GATATAGAAGGGAACTATGAATGTACCCCATGCCCGATGGGGTCGAGCAC
AAAATTTGAAGGATCATACAATTTTAGCCAATGTCAAAGTCAAGATGAAA
TTTACGTACAAGAATTATTCACAAGCTAGGAAAACAATGATATTGGGGAT
AATGTATTTCCTACCGGTTCTAGTCATTATGGTCCTGTGGATTGTTCACA
ATTCTTTTGTTACAAAAAACAATTTGTTGAATGACATATATGACATGCAA
TTAGAATTGGGGAAAATAGTTTTTATGATGAAATACAAGGAAAATCAAAT
GAAGGAAATGGTCAATGAGAGAAGAGCTCTTTCAAATGAAGTCTATTTGA
CTGATTCGTATGAAAAATAGATTTATATAATAAAGTTGTCATCTGTCATC
ATCATCCGATCTGTTTGCGTTCAGCAAACATTCTCTAAATCTGCTAATCT
TTTATGATTACAACTGAGGAATGTCCAATATCAAATGTGGCCGTTGTTTA
AATTGTTA
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protein sequence of SMED30027133-orf-1

>SMED30027133-orf-1 ID=SMED30027133-orf-1|Name=SMED30027133-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
MNVPHARWGRAQNLKDHTILANVKVKMKFTYKNYSQARKTMILGIMYFLP
VLVIMVLWIVHNSFVTKNNLLNDIYDMQLELGKIVFMMKYKENQMKEMVN
ERRALSNEVYLTDSYEK*
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protein sequence of SMED30027133-orf-2

>SMED30027133-orf-2 ID=SMED30027133-orf-2|Name=SMED30027133-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=409bp
SDLFIHLLLTQFFHLNVTTSQRSVINPSINEYYQTKNSKLYYKKTFTTIL
VYYHMILIHSMVTLSCIDQHDNPFGSDVYLTNVSWFSKGEPIFKSDFVRS
YVDLFGFIALLPTKSGQFQILCIGKYKDVNGAMKNASVAHIFNVNDYSIH
VNSLSLDLSVAYFKQNNASMTNVTISESDRRLHYRIFLDNRIKPCSFLFQ
VRFKKKVELFYSQICVRNQQICERESINFYDCTYNELDLIVNISMDISYY
YDYRKINILAPVMDFDNKNEGEAKIRNMTLKQTSNFIKDFFQREFQHFAD
RLVITNTTRFKSEIFCIGTASLLDQENNQSCVLCGVGTFVAAFYAAVAMT
YKKSGFCKLCPKNHYSDIEGNYECTPCPMGSSTKFEGSYNFSQCQSQDEI
YVQELFTS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
Vocabulary: INTERPRO
TermDefinition
IPR011641Tyr-kin_ephrin_A/B_rcpt-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR011641Tyrosine-protein kinase ephrin type A/B receptor-likeSMARTSM01411GCC2_GCC3_2coord: 352..391
e-value: 1.8E-10
score: 50.8
IPR011641Tyrosine-protein kinase ephrin type A/B receptor-likePFAMPF07699Ephrin_rec_likecoord: 351..391
e-value: 3.1E-9
score: 36.5
NoneNo IPR availableGENE3DG3DSA:2.10.50.10coord: 343..401
e-value: 2.2E-6
score: 29.6
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..17
score: 0.575